Transcription factor binding sitesBioinformatics toolsPerformance evaluationThe precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years...
We have evaluated a set of transcription factor binding site prediction tools that could be downloaded and installed locally, identifying FIMO and MCAST as the best-performing tools for identifying individual TFBSs and clusters of TFBSs respectively. While it is possible that there is some inter-re...
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinformatics. 2018;34:2867–9. Article CAS Google Scholar Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, et al. Lisa: inferring transcriptional regulators through integrative modeling of public ...
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal - GitHub - loosolab/TOBIAS: Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
A transcription factor (TF) is a sequence-specific DNA-binding protein that modulates the transcription of a set of particular genes, and thus regulates gene expression in the cell. TFs have commonly been predicted by analyzing sequence homology with the DNA-binding domains of TFs already character...
DeepTFactor predicted 332 candidate TFs in Escherichia coli K-12 MG1655. Among them, 84 candidate TFs belong to the y-ome, which is a collection of genes that lack experimental evidence of function. We experimentally validated the results of DeepTFactor prediction by further characterizing genome...
Machine learning for regulatory analysis and transcription factor target prediction in yeast High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps鈥攖he ident... Dustin,T.,Holloway,... - 《Systems & Synthetic Biology》...
In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res. 2011... M Keiichi,Y Takuhiro,S Tetsuya,... - 《Dna Research》 被引量: 180发表: 2011年 In silico Analysis of Transcription Factor Repertoire ...
pathways, HaCaT cells displayed enrichment in genes involved in fibroblast growth factor receptors, typical of self-sufficiency in growth factor; cytochrome P450 related genes, which are a group of enzymes involved in skin protection60,61,62; DNA strand elongation and VEGFR vascular permeability and ...
The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (mod ENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely...